[Chimera-users] depict hydrophobicity surface in super large molecules in chimera

MARTA PEREZ ILLANA marta.perez at cnb.csic.es
Mon Oct 14 01:31:19 PDT 2019

Thanks a lot Elaine. I just downloaded and was playing around  
yesterday with ChimeraX and it really made my needs!

I hope I will get used to use the commands within rather than user  
interface soon...

Elaine Meng <meng at cgl.ucsf.edu> escribió:

> Hi Marta,
> Two general choices:  use Chimera molmap surface or use ChimeraX,  
> which does not have the molecular surface calculation problems.   
> Also ChimeraX calculates a molecular lipophilicity potential (MLP)  
> that varies through space analogous to ESP instead of just using  
> amino acid lookup values like Chimera.
> The Chimera amino acid lookup values are shown in this table,  
> kdHydrophobicity column.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html>
> (1) in Chimera just color the “molmap” surface by hydrophobicity.   
> In this case it is two steps, though: first you have to color the  
> atoms by amino acid hydrophobicity, and then use color zone to make  
> the surface coloring match the nearby atom coloring.  Also be  
> careful when you make the molmap surface that it is calculated only  
> from protein atoms (not solvent, ligands, …).  Details of the two  
> steps:
>      (A) color atoms by hydrophobicity with Render by Attribute  
> (menu: Tools… Depiction… Render by Attribute, and in that dialog  
> choose to color atoms by residue attribute kdHydrophobicity) or  
> “rangecolor” command, e.g.
> rangecolor kdHydrophobicity min dodger blue 0 white max orange red #3
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#render>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html>
>      (B) use Color Zone (menu: Tools… Volume Data… Color Zone) to  
> make the molmap surface coloring match the atom coloring, or command  
> “scolor zone” e.g. if molmap is #3.1 and atoms are #3:
> scolor #3.1 zone #3&protein range 5
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzone.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html#zone>
> (2) get ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>, open your  
> structure, show surface (e.g. command “surface”), and color by MLP  
> (e.g. command “mlp”).
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/mlp.html>
> Alternatively in ChimeraX you can just color by the amino acid  
> kdHydrophobicity values like in Chimera using this script provided  
> in the ChimeraX User Guide as an example of a custom preset (just  
> save the file *.cxc and then open it in ChimeraX to run it):
> <http://rbvi.ucsf.edu/chimerax/docs/user/kyte-doolittle_hydrophobicity.cxc>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>> On Oct 13, 2019, at 7:09 AM, Marta Perez Illana  
>> <marta.perez at cnb.csic.es> wrote:
>> Hi all
>> I was trying to analyze the hydrophobic surface of two very large  
>> structures ( 3 chainsx 900 aa each so 2.700aa). As expected the  
>> default surface calculation has failed. Normally for electrostatic  
>> potential what works for me is making a mol map (molmap  #3  4  
>> gridSpacing  0.5) and then calling the pdb2pqr and apbs servers  
>> directly from chimera, which is very convenient.
>> However I cannot find an analogous way to make it with  
>> hydrophobicity... Since the surface fails for such big molecules,  
>> the straight forward way (present-3interactive surface  
>> hydrophobicity) does fail as well...
>> Then... is there any server than can be called from chimera, to get  
>> hydrophobicity as an attribute to be depicted? Or alternatively  
>> could you suggest any server that gives output hydrophobic column,  
>> compatible  to get it after to chimera attributes? Reading a bit I  
>> found that, not as electric fields, that can be computed for  
>> structures, hydrophobicity comes just for the sequence, without  
>> taking into account the neighbours and context...
>> P.D: I have managed to represent in other programs the hydrophobic  
>> surface, but I really want to make it in chimera, to make it more  
>> consistent and easy to organize myself...
>> Thanks a lot! and sorry if the question goes beyond Chimera...
>> Marta

Marta Pérez Illana, Ph. D. student
Dept. of Macromolecular Structures Lab 15
Centro Nacional de Biotecnología (CNB-CSIC)
Darwin, 3
28049-Madrid (SPAIN)
Email:  marta.perez at cnb.csic.es
Phone:  (0034) 91 585 4508

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